Gabriele Sales
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/spatialDE |
| git_branch: RELEASE_3_17 |
| git_last_commit: be7acd4 |
| git_last_commit_date: 2023-04-25 11:32:03 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:41 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1972/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialDE 1.6.0 (landing page) Gabriele Sales
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the spatialDE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: spatialDE |
| Version: 1.6.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialDE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings spatialDE_1.6.0.tar.gz |
| StartedAt: 2023-10-16 07:06:01 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 07:10:48 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 286.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: spatialDE.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialDE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings spatialDE_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'spatialDE/DESCRIPTION' ... OK
* this is package 'spatialDE' version '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'spatialDE' can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See 'F:/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
spatial_patterns 10.82 0.89 5.86
FSV_sig 4.14 2.16 30.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck/00check.log'
for details.
spatialDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL spatialDE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'spatialDE' ... ** using non-staged installation via StagedInstall field ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (spatialDE)
spatialDE.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(spatialDE)
>
> test_check("spatialDE")
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
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result = func(self.values, **kwargs)
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74%|███████▍ | 74/100 [00:00<00:00, 338.28it/s][A
[A
Models: 90%|█████████ | 9/10 [00:02<00:00, 3.17it/s]
0%| | 0/100 [00:00<?, ?it/s][A
39%|███▉ | 39/100 [00:00<00:00, 356.56it/s][A
79%|███████▉ | 79/100 [00:00<00:00, 361.95it/s][A
[A
Models: 100%|██████████| 10/10 [00:03<00:00, 3.33it/s]
Models: 100%|██████████| 10/10 [00:03<00:00, 3.28it/s]
Models: 0%| | 0/10 [00:00<?, ?it/s]
0%| | 0/100 [00:00<?, ?it/s][A
47%|████▋ | 47/100 [00:00<00:00, 429.71it/s][A
[A
Models: 10%|█ | 1/10 [00:00<00:01, 4.92it/s]
0%| | 0/100 [00:00<?, ?it/s][A
28%|██▊ | 28/100 [00:00<00:00, 254.92it/s][A
68%|██████▊ | 68/100 [00:00<00:00, 319.98it/s][A
[A
Models: 20%|██ | 2/10 [00:00<00:02, 3.74it/s]
0%| | 0/100 [00:00<?, ?it/s][A
36%|███▌ | 36/100 [00:00<00:00, 329.13it/s][A
71%|███████ | 71/100 [00:00<00:00, 323.77it/s][A
[A
Models: 30%|███ | 3/10 [00:00<00:01, 3.56it/s]
0%| | 0/100 [00:00<?, ?it/s][A
35%|███▌ | 35/100 [00:00<00:00, 319.97it/s][A
70%|███████ | 70/100 [00:00<00:00, 320.01it/s][A
[A
Models: 40%|████ | 4/10 [00:01<00:01, 3.41it/s]
0%| | 0/100 [00:00<?, ?it/s][A
35%|███▌ | 35/100 [00:00<00:00, 319.99it/s][A
70%|███████ | 70/100 [00:00<00:00, 319.17it/s][A
[A
Models: 50%|█████ | 5/10 [00:01<00:01, 3.33it/s]
0%| | 0/100 [00:00<?, ?it/s][A
35%|███▌ | 35/100 [00:00<00:00, 319.97it/s][A
68%|██████▊ | 68/100 [00:00<00:00, 309.24it/s][A
[A
Models: 60%|██████ | 6/10 [00:01<00:01, 3.26it/s]
0%| | 0/100 [00:00<?, ?it/s][A
34%|███▍ | 34/100 [00:00<00:00, 339.22it/s][A
68%|██████▊ | 68/100 [00:00<00:00, 338.97it/s][A
[A
Models: 70%|███████ | 7/10 [00:02<00:00, 3.28it/s]
0%| | 0/100 [00:00<?, ?it/s][A
33%|███▎ | 33/100 [00:00<00:00, 329.24it/s][A
66%|██████▌ | 66/100 [00:00<00:00, 328.92it/s][A
99%|█████████▉| 99/100 [00:00<00:00, 328.90it/s][A
[A
Models: 80%|████████ | 8/10 [00:02<00:00, 3.28it/s]
0%| | 0/100 [00:00<?, ?it/s][A
39%|███▉ | 39/100 [00:00<00:00, 354.91it/s][A
75%|███████▌ | 75/100 [00:00<00:00, 338.84it/s][A
[A
Models: 90%|█████████ | 9/10 [00:02<00:00, 3.36it/s]
0%| | 0/100 [00:00<?, ?it/s][A
36%|███▌ | 36/100 [00:00<00:00, 327.73it/s][A
76%|███████▌ | 76/100 [00:00<00:00, 349.15it/s][A
[A
Models: 100%|██████████| 10/10 [00:02<00:00, 3.41it/s]
Models: 100%|██████████| 10/10 [00:02<00:00, 3.41it/s][ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
46.29 2.40 58.78
spatialDE.Rcheck/spatialDE-Ex.timings
| name | user | system | elapsed | |
| FSV_sig | 4.14 | 2.16 | 30.06 | |
| mockSVG | 0.31 | 0.02 | 0.28 | |
| modelSearch | 2.52 | 0.32 | 1.53 | |
| model_search | 1.96 | 0.22 | 1.09 | |
| multiGenePlots | 2.46 | 0.22 | 1.69 | |
| regress_out | 0.17 | 0.02 | 0.14 | |
| run | 1.02 | 0.14 | 0.58 | |
| spatialDE | 1.32 | 0.11 | 0.77 | |
| spatialPatterns | 1.21 | 0.12 | 0.70 | |
| spatial_patterns | 10.82 | 0.89 | 5.86 | |
| stabilize | 0.93 | 0.03 | 0.78 | |